Chromosomal rearrangements are key players in human health, having impacts in human fertility, cancers, and other diseases. Here we use an evolutionary approach to study chromosomal rearrangements and their potential to produce advantageous and detrimental cellular changes using Drosophila as a surrogate. We will sequence multiple populations of Drosophila from three different species and identify chromosomal rearrangements in each strain. We will determine whether genes in specific functional classes are more likely to be associated with rearrangements and whether specific genetic mechanisms influence their formation. We will use simulations and modeling to develop a framework to detect rearrangements that have been favored by selection. We will modify existing population genetic methods to correct for effects of demography, differential recombination, partial selective sweeps and other factors. We will then use RNA-sequencing to determine whether these selectively favored mutations are likely to be associated with changes in gene expression. In a second specific aim we will determine the extent to which rearrangements influence the results of artificial selection. We will identify rearrangements in selected and control strains, and compare the genetic background to wild-type strains of D. melanogaster. This specific aim should explain whether genetic background correlates with selective outcomes and the extent to which pleiotropy limits evolution in nature. These methods will produce an in-depth view of chromosomal structural variation among species and will determine the ways in which they influence adaptation. Furthermore, we will establish new analytical methods that can more accurately identify selected regions, a result that can be applied to whole genome screens of selection in a large number of organisms. We will also link rearrangements to regulatory effects and will determine how this influences selective impacts.